AMBER Archive (2009)

Subject: AW: AW: [AMBER] atomtypes in gaff

From: Aust, Susanne (
Date: Thu Jun 25 2009 - 06:27:19 CDT

Dear Francois,
I load the complex in xleap as pdb, so no name is necessary.
At my first trail I load the wrong pdb with ZNB in the pdb. I correct this to
ZNA (like in my ZNA.lib) and load the pdb again and then everything was read
in without error.
The ligand in the complex has the name ABI. The parameter for this ligand I
read in to xleap with loadamberparams bzim_correct.frcmod and loadamberprep
When I prepare my complex in xleap, there is no error and the pdb or mol2
from xleap looks o.k.
But after the minimization the ligand is not coordinated. With a wrong
benzimidazole-structure (the double bonds are not on the correct positions)
the ligand keeps coordinated.
It's difficult for me, to describe the problem, because I don't know exactly
at which position of the preparation line the failure occurs.

-----Ursprüngliche Nachricht-----
Von: []Im
Auftrag von FyD
Gesendet: 25 June 2009 12:33
An: AMBER Mailing List
Betreff: Re: AW: [AMBER] atomtypes in gaff


You need to add a molecule name to your Tripos mol2 file (I wonder if
this is not a bug in the savemol2 command because you have many
  3263 3293 228 0 1

> The atomtypes should be correct.
> I send you the mol2 file of the comlex from xleap.
> The benzimidazole is over the N3 (nd) non physical coordinated to the zinc.
> I calculate other ligands (substrate and imidazole derivative) with this
> enzyme and it works.
> So I think it is not a problem of zinc.
> I hope, this is the file you want.
> I send you also the xleap.log

In your LEaP log file, you load the Zinc FF library:
loadoff ZNA.lib

In your Tripos mol2 file, your Zinc is defined as ZNB (residue name,
FF atom type & atom name). Consequently, in LeaP you get this message:

Unknown residue: ZNB number: 225 type: Terminal/last
..relaxing end constraints to try for a dbase match
   -no luck
(Residue 226: ZNB, Terminal/last, was not found in name map.)
Unknown residue: ZNB number: 226 type: Terminal/last
..relaxing end constraints to try for a dbase match
   -no luck

Then, you load the frcmod file for your zinc atom:
Loading parameters: ./frcmod.zna
Reading force field modification type file (frcmod)
Reading title:
This frcmod file is for ZNA (zinc 2+ ion).

I wonder if the FF atom type of Zn is well defined.

=> add
addAtomTypes {
          { "ZN" "Zn" "sp3" }
      or what is required...

I do not know if these are the reasons of your problem. However, you
might correct these problems to see if this helps.

regards, Francois

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